


The Unexpected was Expected

by Vickymil



Category: Doctor Who, Doctor Who (2005), Supergirl (TV 2015)
Genre: Crossover, Doctor Who Series 3, Post-Supergirl (TV 2015) Season 2, arrowverse
Language: English
Status: In-Progress
Published: 2021-01-04
Updated: 2021-03-08
Packaged: 2021-03-15 05:54:59
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 10
Words: 13,247
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28558674
Author URL: https://archiveofourown.org/users/Vickymil/pseuds/Vickymil
Summary: What happens when two different alien crime stoppers meet? Tensions are high and the teams are having a hard time working together. Will they be able to save the world without delicate friendships going down in flames?
Comments: 26
Kudos: 30





	1. Chapter 1

**Author's Note:**

> Here we are again! I started working on this over the winter break after I looked through this website to find more of this type of crossover and couldn't find many. Please tell me what you think!

**TARDIS**

"Where are we now?" Martha asked with a huge smile on her face, the mystery of travelling with the Doctor was her favourite bit.

"National City, America, 2017," The Doctor said scratching the back of his head.

"I was expecting to see the purple seas of some exotic planet, but we ended up in America," Martha said giggling, it was enjoyable to watch the Doctor try and figure out why he couldn't pilot the TARDIS.

"It seems she has a mind of her own today. Let's go see where we landed," The Doctor said grabbing his coat off of one of the support beams and practically running towards the doors with Martha on his heels.

When they emerged from the depths of the TARDIS they were greeted with the foul smell of a back alley.

"Doctor, why do you always land in a back alley? They stink!" Martha said plugging her nose.

"Come on then Martha, let's have a look around," The Doctor said stuffing his hands back into his pockets. The smell didn't even bother him despite having a stronger sense of smell than humans.

They eagerly walked around the corner and out of the alley. A new city in a new time, Martha never got tired of seeing new locations, even if she was still pretty close to modern-day London the Doctor had a way of making her see things differently.

"Ah American cities," The Doctor began, "They all begin to look the same after a while, and smell the same. But there's something about National city that makes it special. Can't remember what..." The Doctor trailed off.

Martha was only listening to the Doctor with one ear, she was too busy looking around at all of the skyscrapers around her. This was technically 10 years in her future, it was a marvel.

Suddenly something flew overhead.

"What's that?" Martha asked as she jumped into the Doctor's arms.

The Doctor smacked his forehead, "How could I forget! That was Supergirl!"

"Would you care to elaborate?"

"Yeah. Supergirl is an alien from Krypton and she's known as the defender of National City."

"So she's an alien who flys around and defends people from what?"

"Mostly mundane things like robberies and muggings. But there are a lot of alien incidents in National city that she deals with as well."

"Like hostile aliens?"

"Exactly."

"So she's kind of like you then. You know saving people from aliens."

"Perhaps. But she'd rather punch her way out of problems. I like to solve them."

"True. What is there to see in National City?" Martha asked changing the subject as the Doctor had begun to emotionally distance himself from the conversation.

**DEO**

Winn Schott was typing away at his computer when an alert popped up. No, two alerts popped up.

"What is it, agent Schott?" Director J'onn J'onzz asked coming in from another room. He could be a bit intimidating, after all, he was the Martian Manhunter, the last son of Mars.

"We just received two notifications. One is of alien space crafts hovering just above Earth. And the other is of multiple unknown readings coming from this section of the city," Winn said pointing to the screen.

"Supergirl," The Director called into the comms.

"What's up J'onn?" She said as she slowed down her speed to hear J'onn better.

"There are some strange readings coming from your part of the city. Could you check them out?"

"On it."

"Winn, I want you to do some more in-depth scans of what's in the sky. I want to know what we're dealing with before it comes."

**Above National City**

Supergirl had pulled a U-turn, she had already flown over that part of the city and didn't see anything out of the ordinary but she wanted to double-check. She was flying pretty fast now, the wind blowing through her hair was the best feeling in the universe. She slowed down now so she could have a close look at what was below her. Good thing she decided to double-check, a cable had snapped and sent a steel beam caravaning towards the ground. She dove after it, then passed it. As she was about to catch it she heard a voice that had a strange accent.

"Martha look out!" He shouted as he noticed the steel beam falling towards them. The woman beside him, Martha, looked up as the man moved in front of her protecting Martha from the steel beam.

Supergirl caught the beam with ease and flew it back up to the crane and set it down where it was meant to.

"Thank you!" Martha shouted and the man raised his hand in thanks. She could only hear Martha because of her super hearing but they both genuinely looked happy that she had saved them.

 _Maybe I should write an article about what tourists think of Supergirl_. That was Kara thinking, Supergirls alter-ego a reporter for CatCo magazine. She could go interview Martha and whoever that man was with her.

She snapped out of her reporter thoughts quickly and looked around for anything unusual coming up empty-handed.

"Hey, J'onn," Supergirl said heading back towards the DEO

"Go ahead Supergirl."

"I didn't see anything suspicious. I'm heading back to the DEO."

"Okay, Supergirl."

**DEO**

Supergirl landed on the balcony and sauntered into the DEO.

"Hey Kara," Alex said walking up to her sister, "How'd it go?"

"Nothing out of the ordinary. But I saved these two British tourists and I'm going to interview them and write a piece on what tourists think of Supergirl."

"That sounds like a good idea. But you never know what they're going to say."

"Don't worry, I can handle myself."

"Supergirl, agent Danvers," J'onn said calling them over, "Do either of you recognize these energy signatures?"

Kara shook her head.

"No," Alex said, "But whatever it is it must be pretty big to be giving off that much energy."

"But I didn't see anything that big when I was flying over the city."

"Then it must be in a building," J'onn concluded, "Winn any luck on identifying the space crafts?"

"No, they're not in our database," Winn said spinning around in his chair, "Neither is that strange energy coming from somewhere downtown."

"Well, you guys have fun figuring this out. I have an idea for an article," Supergirl said walking out of the room, "Call me if you need anything."


	2. Chapter 2

**Notes for the Chapter:**

> We're back! I forgot to tell you that I'll be updating every Monday, hopefully. Let me know what you think and enjoy!

**Unexpected Cafe**

"That was freaky," Martha said as they walked into the nearest cafe.

"We would have been pancakes," The Doctor said following Martha up to the counter.

"Welcome to the Unexpected Cafe! What can I get for you today?" The young woman behind the counter asked.

"Two teas please," Martha replied.

"Are you two all right, you seem pretty shaken up?"

"Yeah. Although we almost got crushed by a steel beam," The Doctor replied in his normal bumbling way, he was not good with conversational talk.

"When you say almost you mean that Supergirl saved you, yeah?"

"Yeah," Martha said, "We were pretty lucky. It was still pretty freaky though."

"I can imagine. I've lived in National City my entire life and have never been saved by Supergirl. I've always wanted to meet her."

"Why's that?" Martha asked. The Doctor had wandered off at this point to go look at a bookshelf.

"She saved my best friend from an explosion, I just wanted to thank her," The cashier smiled, "Here, have the teas. On the house."

"Thank you. What's your name?"

"Iva."

"Nice to meet you, Iva. I'm Martha and that's the Doctor" Martha said pointing over her shoulder.

"Have a good day," Iva said with a smile.

"You too. Thanks again," Martha said grabbing the teas and going to sit down at a table in the corner.

"You know what I can't seem to figure out. Why did the TARDIS bring us here?" The Doctor said sliding into the seat across from Martha.

"You're telling me you didn't plan for us to end up here?"

"Not exactly. She always takes us to where we need to be."

"You're trying to figure out why she brought us here?"

"Exactly."

"Maybe she wanted us to relax a bit."

"Maybe," the Doctor said rubbing his chin, not entirely convinced.

Then the bell above the door to the cafe chimed and a blonde-haired woman wearing glasses walked in. She looked around until her eyes landed on the Doctor and Martha.

"Hi there. My name is Kara Danvers and I'm a reporter with CatCo magazine, do you mind if I ask you a few questions?"

"Sure," The Doctor said, "What for?"

"I wanted to get tourists' perspectives on Supergirl. She told me she saved you two this morning from a falling steel beam."

"You know Supergirl?" Martha asked.

"Yes, we're close friends," Kara said pushing up her glasses.

"That must be pretty cool."

"It is. Do you guys mind if I record?" Kara said pulling out a recorder from her bag.

"Not at all," Martha said looking over at the Doctor.

"Before we start, what are your names?"

"I'm Martha Jones and that's-"

"John Smith," The Doctor said as 'The Doctor' was not really a name.

"All right. So what brings you to National City?" Kara asked, a little suspicious of John Smith.

"We were just passing through," The Doctor said.

"We travel a lot," Martha continued.

"What are your opinions of Supergirl?"

"Well, I think she's marvellous," The Doctor began, "The way an alien has become a beacon of hope in such a big way for such a large community is fantastic. And the way she saves people from everyday accidents is really kind of her."

"You seem to know a lot about Supergirl for someone passing through."

"I do a lot of reading."

"And what are your thoughts on Supergirl, Martha?"

"I'm really thankful she saved our lives. But it's amazing how she goes around helping people. I know someone else like that, and he's really good at what he does," Martha said looking over at the Doctor who returned her gaze with a small smile. Kara noticed this little exchange making a mental note of it.

"Also," Martha continued, "It's nice to see how many people she has touched with her actions. That cashier, Iva, said that Supergirl saved her best friend from an explosion. Supergirl has probably touched everyone's lives in this city one way or another and I think that's pretty cool."

"Thank you, those are some very inspiring words." Kara paused for a moment, she was not expecting that sort of response from these two, "Just one more question, where are you guys from?"

"London, England," Martha said, "And can you tell Supergirl 'Thank you' from us?"

"I'm sure she already knows," Kara replied turning off her recorder.

"How many aliens are there in National City?" The Doctor asked.

Kara hesitated a little bit, "I'm not sure but I know there are a few. Thank you for your time," Kara said as she stood up, "It was nice meeting you."

"It was nice meeting you as well," Martha said as Kara turned around and smiled then walked out.

Once Kara left the Cafe the Doctor spoke, "That was a bit odd."

"What do you mean?"

"How did she find us so fast?"

"Good point, it all happened a bit too fast."

"Let's head back to the TARDIS, I want to find out just how many aliens are in National City."

**TARDIS**

The Doctor paused outside of the TARDIS and pulled out his key while Martha threw out their empty cups into a nearby dumpster.

"Why are we scanning for alien life forms, Doctor?"

"Something is off here and I want to know what," The Doctor said as the TARDIS door opened and they walked inside. The Doctor threw his coat over one of the large pillars that filled the room, Martha always thought that it was a bit bizarre to throw his coat when he had a coat rack by the door.

The Doctor was at the central console in an instant pushing buttons and pulling levers and looking at his screen.

"But how is scanning for alien life forms going to help?"

"I'm pretty sure that reporter was hiding something when I asked her about aliens in National City, and I want to find out what."

Then the Doctor started scanning, "Would you look at that," He muttered.

"What is it?" Martha asked moving look at the screen.

"There are hundreds of aliens in National City and loads of alien technology! There are multiple different species and I'm pretty sure most of them are refugees! It's wonderful!"

Martha was beginning to understand some of the reading on the screen, "It looks like there is a big cluster of alien stuff right there," Martha said pointing at the screen.

"Yeah, I wonder what it could be?" The Doctor said scratching the back of his head. Then the TARDIS made a weird noise and highlighted a part of the map for the Doctor.

"That's not good," he mumbled

"Why what is it?"

"There's a fleet of ships in Earth's orbit, doesn't look like they have been detected."

"I guess we have to go check it out," Martha said.

"Yeah, but not from in here. I don't have good enough readings to know what we're dealing with."

"Then from where," Martha asked.

From that cluster of alien tech, they're bound to have what we need. Allons-y!" The Doctor said as he practically ran towards the doors, grabbing his coat in stride.

They came to a sudden halt outside the door, with Martha just closing the doors before she was told to hold up her hands. They were staring down the barrel of multiple guns and people dressed in all black attire.


	3. Chapter 3

**Notes for the Chapter:**

> Here is the next chapter! I hope you enjoy it! Thanks to everyone who left comments and kudos, they mean so much!

**DEO**

Winn had been running any program he could think of to figure out what kind of energy the signature could be. All he could tell was this energy wasn't harming anything. As he was staring at his screen another alert popped up. In the center of the unknown energy field, someone was initiating some sort of scan.

"Hey J'onn," Winn called.

"What is it, agent Schott?" J'onn asked coming over.

"There is a scanning signal coming from the middle of the unknown energy field," Winn said, his voice becoming a little anxious.

"Agent Danvers," J'onn called.

"What is it, sir?" She said walking over.

"I want you to lead a team and investigate what is causing that signal. It's probably what's causing that energy field as well."

"On it."

Within minutes Alex Danvers and her team were combing an alleyway for the source of this signal. Winn was with her with some sort of device used to pinpoint the location. They rounded a corner in the alleyway and Winn's machine started to beep.

"Whoa," Winn said checking the readings on his device, "We're getting close."

The more they moved along the closer the beeps got to each other until they got to a big blue box, then Winn's device made a screeching noise.

"The signal is coming from in there."

"Are you sure?" Alex asked, wondering what type of energy a big blue police box could be emitting.

"Positive."

Alex motioned for the soldiers around her to surround the box with guns at the ready. Before she could get close to the box a man in a brown suit and lighter brown jacket came out of the box, followed by a young woman wearing a purple leather jacket and jeans.

"Put your hands where I can see them," Alex shouted and they both did so. The man looked confused, while the woman looked scared, although she was trying to hide it.

"Are you the owners of the police box?" Alex asked.

"That would be me," The man replied with a British accent, "And I really don't like guns, could you put them down?"

Alex contemplated doing that-they certainly didn't seem like a threat, but she would have to search them for weapons nonetheless.

"Are you carrying any weapons?" Alex asked her gun still trained on the man.

"No, I don't like weapons and I like them even less when they're pointed at me and my friend," he said.

Alex lowered her gun, "I believe you but I still have to search you," Then she nodded at two of her guys to go and search them. The man seemed to be a little more at ease but the woman still looked scared.

Alex turned around to look at Winn, "Find anything?"

"No, but the scanner has stopped, I need to get inside to find out what we're dealing with."

Alex turned around to see that no weapons had been found on the suspects.

"If you don't mind me asking," the man started, "Who are you?"

"I'm agent Alex Danvers with the department of extranormal operations. Who are you?"

"I'm Doctor John Smith and this here is Martha Jones."

"Well then, Doctor Smith and Ms. Jones you're coming with us," Alex said turning towards her agents, "You four stay here with agent Schott. You three come with me." Alex turned around and walked back out of the alleyway.

"You be careful with her," The Doctor said pointing to Winn as he was scanning the TARDIS.

Winn wasn't really sure what to be careful of after all it was just a big wooden box and just ignored the comment.

**CatCo**

Kara was sitting at her desk listening to her interview with the British tourists; they said lovely things about her and it made her smile. She had lost track of how many times she had listened to it. She was about to restart the recording when her phone went off. It was Alex.

"Hey what's up?" Kara asked with a bit of a giggle.

"Were the people you interviewed Dr. John Smith and Martha Jones?"

"Yeah, why?"

"We have reason to believe they're behind the strange energy signature."

"I'm on my way," Kara said angrily, how could people who said such nice things about her be planning something sinister. She angrily packed up her things and headed towards the DEO.

**DEO**

The Doctor and Martha were lead into the DEO by Alex and taken into an interrogation room. They sat there for a bit while Alex went to get J'onn.

"We have two suspects in the interrogation room."

"Where did you find them?"

"They came out of the thing that was emitting the strange energy."

"What was this thing?"

"That's the strange thing, it was a big blue wooden police box."

"That is strange, Alex. Let's go talk to them."

Alex and J'onn walked into the interrogation room.

"Don't worry Martha, everything will be fine."

"Every time you say that Doctor, things aren't fine for a while!"

"Of course they are!"

"What about that museum incident?"

"Well..." The Doctor said rubbing his chin.

J'onn looked over at Alex thinking this was a good time to intervene.

"I'm Director J'onn J'onzz of the DEO. You've already meet agent Danvers," J'onn said introducing himself with the name of the human he has shapeshifted into.

"Yes, we have. I'm Doctor John Smith and this is the lovely Martha Jones. Why did you bring us here?" The Doctor said trying to be friendly.

"So you can answer a few questions," J'onn said in a very stern voice.

"If you wanted to ask us questions, you could have just asked us in a cafe like that reporter did," Martha said. Alex made a mental note to not underestimate Martha, she seems to be just as smart as Doctor John Smith.

"See Martha, never trust acronyms. You never know what they're hiding." Martha just rolled her eyes.

"I don't think you understand the seriousness of the situation, Mr. Smith." J'onn was pretty sure it was a fake name and what Mr. Smith said next confirmed it.

"It's just the Doctor." J'onn looked a little confused, "I go by the Doctor."

"So people call you 'Doctor'?" Alex asked.

"Yeah," He said nodding.

"So why are we here?" Martha asked, trying to get out of here as quickly as she could.

"We discovered strange energy coming from your police box," J'onn said crossing his arms.

"You did?" The Doctor said with a surprised and confused look on his face, "There shouldn't be any energy coming from..." The Doctor slapped his forehead, "That's why we've been having to fuel up so often! The engines haven't been shutting properly and leaking Artron energy!"

"Artron energy, is it harmful?" Alex asked.

"No! Not at all!" The Doctor said defensively.

"I've never heard of Artron energy, what is it?" J'onn asked.

"It's time travel energy," The Doctor said cautiously.

"You're a time traveller," Alex said, "What year are you from?"

"I don't know what year he's from but I'm from 2007," Martha said with a bit of a chuckle. The room went silent, Alex was trying to take in the fact that they were time travellers with a police box time machine. But J'onn was trying to validate the story, he could read Martha's mind and knew she was telling the truth but he couldn't read the Doctor's mind. Naturally, J'onn pushed a little harder but he was pushed back with just as much force. He looked over at the Doctor to see him concentrating. A normal human shouldn't have been able to resist his telepathy, perhaps this Doctor really was from the future.

The Doctor was aware of someone trying to read his mind and he didn't like it, no way was Alex doing it, she was checking something on her phone and he was pretty sure she was human anyway. It obviously wasn't Martha, but the mind reader probably already read her mind. That only left J'onn, no human could possess those abilities, he had to be alien. Then some words came to mind, those of an old friend. _A door, once opened, one may step through in either direction._ If J'onn got into his mind he could step through into his. But he wasn't going to let that happen, he had too many secrets to be kept safe.


	4. Chapter 4

**Notes for the Chapter:**

> Thank you guys for all of your support! I hope you enjoy this chapter and tell me what you think!

**Alleyway**

Winn had been trying to get into the police box for what felt like forever. The door read _pull to open_ but when he pulled it, it didn't budge. Then he pushed it with no luck either. Then he tried picking the lock. The lock was a lot more complicated than it looked, so Winn got one of the soldiers to shoot the lock. Nothing, not a scratch... and it's just a wooden box! Winn was getting fed up; he should be able to get into a wooden box without any problems. He grabbed an alien artifact from his bag. He had been trying to figure exactly what it did but he knew it could cut through very dense materials. To make sure it was working he took a bucket from a nearby dumpster and cut several holes in it like the Flex Seal commercials but he didn't have any Flex Seal with him to fix the bucket. Too bad he didn't have a boat.

He went up to the box and decided to cut around the lock. But when he used it there wasn't a scratch on the box, not a scorch mark, not a small indentation, nothing. He let out a sigh; he was trying so hard not to get frustrated but he was running out of ideas to get into the box. He let out a yelp when his phone went off and fumbled for it.

"Hey, Alex, what's up?" Winn said into the phone.

"I'm fine. You're on speaker with J'onn. What did you find in the box?"

"That's the problem. I can't get into the box."

"The box is made of wood Winn. This better not be a joke."

"Seriously, I can't get into the box."

"Have you just been clowning around for the past hour agent Schott?" J'onn asked, he sounded angry.

"No. The lock wouldn't budge when we tried to pick it. Even the alien lock picker couldn't do it. Then I used the unidentified alien artifact on the box and it didn't leave a scratch."

"Which unidentified artifact?"

"The destructive one you told me shouldn't leave the DEO."

There was a moment of silence. Winn was waiting for J'onn to yell at him or something. But J'onn was surprised that the unidentified artifact couldn't break into the box.

"Winn, report back to the DEO. You can get back to the box later."

"Okay-" Then J'onn hung up. Winn sighed, "Let's head back to the DEO J'onn's orders."

**DEO**

J'onn hung up the phone and sighed.

"J'onn what's wrong?" Alex asked, genuinely concerned.

"Winn should have been able to get into the box if it were just a box. I don't know what it is and I can't read the Doctor's mind to figure it out."

"Then we should be in there figuring out why," Alex said about to head back into the interrogation room.

"No, I can read Martha's mind, she's telling the truth and believes what the Doctor was saying to be true."

"Then what do we do with them?"

"I don't know, but I'm almost certain the Doctor isn't human. We also have to figure out what is hovering above Earth and deal with that."

**Interrogation Room**

"Do you think they'll let us out?" Martha asked as the Doctor was pacing the room.

"They'll let you go. I think J'onn has figured out that I'm not entirely human. Of course, neither is he but..." The Doctor trailed off.

"If J'onn's not human is he a threat?"

"No. He tried reading my mind but I have stronger physic abilities than humans so I pushed him back."

"Are you saying he read my mind to?"

"Yeah. But without physical contact, it is extremely hard to dig through memories. He was probably checking to see if you were telling the truth. Can you do me a favour?" Martha nodded, "Don't tell them what species I am."

"Why?"

"Some species will try to kill me on the spot and I want to make sure J'onn isn't one of those."

"I don't get it, Doctor, you're a good man."

"Not everyone sees me that way Martha, I've done some horrible things that I'd rather forget."

Martha was silent, she knew that the Doctor had a checkered past but she wasn't about to push the Doctor into telling her.

**Control Room**

Supergirl had just landed and stormed in, she was pissed off at John and Martha for saying nice things about her, then bringing unknown energy into the city. She was about to give them a piece of her mind.

"Supergirl," J'onn called out.

"Where are they?" She asked sounding extremely pissed off.

"Are you alright?" J'onn asked.

"I just need to speak with them."

"Not like that you're not," J'onn said. Supergirl looked like she was about to challenge J'onn when Alex, who had been observing the shouting match came over.

"Kara. Can I have a word?" Alex motioned to the empty medical room. Kara reluctantly followed Alex into the room.

"What?" Kara asked having calmed down only a little bit.

"Why are you so upset?"

"I saved those two, then interviewed them and now look where they are! They were probably planning to destroy the city!" Kara said melting down.

"Kara," Alex said in her kind big sister voice, "J'onn and I interviewed them. They honestly didn't know that their ship was leaking Artron energy. They also said it was harmless."

"Oh thank God," Kara breathed a sigh of relief, "Wait. Did you say Artron energy?"

"Yeah, why?"

"Artron energy was rumoured to be a time travelling energy. I think they started experimenting with some on Krypton."

"Well, that fits their story."

"They're time travellers?"

"We believe so. Martha said she is from 2007."

"Really!" Kara looked excited now, "Now I have to go talk to them!" Kara said turning around.

"Promise you'll be gentle."

"I promise," Kara said with a wide grin. She was getting ready to become the stoic Supergirl and not Kara Danvers.

While Alex and Kara were having a sisterly conversation Winn returned from the alleyway. He walked into the room ashamed that he couldn't get into a wooden box.

"Give it here, Winn," J'onn asked and Winn reluctantly handed the unidentified alien artifact to him, "I'm surprised that this didn't work on a wooden box."

"I tried everything I could think of and nothing left a scratch. Did they tell you what's inside the box?"

"I'm pretty sure it's a time machine of some sort."

"Really?! Awesome!" Winn said with his eyes lighting up, "Can I go talk to them to figure out how to get inside?"

J'onn looked closely at Winn, there was no saying no to him, "Fine, but be quick; we have other matters at hand."

"Thank you!" Winn said practically running towards the interrogation room.

"Hey Winn," Kara called, "Where are you headed?"

"To go talk to our friends with the blue box. So are you, aren't you?"

"Yeah, we can go together."

Kara and Winn walked down the hallway. They didn't notice Alex going to the surveillance room to listen in on their conversation.


	5. Chapter 5

**Notes for the Chapter:**

> Hello again! I hope you enjoy this chapter and feel free to point out any spelling or grammatical errors!

**DEO - Interrogation room**

The Doctor was pacing the room, thinking about how he could have missed closing the engines while Martha sat at the table with her arms crossed, growing more and more impatient. After travelling with the Doctor for so long, where it was just one adventure after another, being stuck in a room for hours bored her quickly.

Suddenly the door burst open and two people walked in but Martha didn't really care who.

"Can we go now?" Martha asked with a hint of annoyance in her voice. Supergirl and Winn were shocked at the request.

"Sorry," Martha said, "I wasn't paying attention. Thanks for saving us earlier."

"Yeah, thank you," The Doctor said, stopping his pacing, "You can tell your friend Kara that she doesn't have to thank you for us."

"It's okay she already told me," Supergirl said a bit flustered, she always got flustered when she had to pretend to communicate with her alter ego, "She also played me the interview with you two, thanks for saying those things about me."

"Well it's the truth," Martha said.

"Which one of you owns the blue box?" Winn asked coming out from Supergirl's shadow.

"That would be me. I'm the Doctor," He said stick out his hand.

"I'm Winn," He said shaking hands, "How do you make wood so strong?"

The Doctor stopped shaking his hand and looked confused.

"I was tasked with getting into your box and I couldn't get in. And there aren't a lot of things I can't do when it comes to technology."

"You tried to get into the TARDIS? Oh, she's not going to like that. Why did you try and get in?"

"There was strange energy coming from it and we wanted to stop it before it could hurt anyone. Then we realized it was harmless."

"Just curious, how did you try and get in?"

"Everything from picking the lock to alien tech."

"Wow, nothing can get through those doors," The Doctor said sounding a bit impressed at himself.

"How do you get inside?"

"I have a key."

"That makes sense. Anyway, I have bigger fish to fry right now so-"

"Do you mean the alien spaces shifts hovering above the Earth?"

That statement caught Supergirl's attention dragging herself from her thoughts. It also caught Alex's attention from the viewing room.

"H-how did you know?"

"The scan I was doing earlier detected them. I'm assuming that's how you found us. We were leaving to check out a place with a lot of alien equipment, which I'm guessing is this place, so we could identify who they were."

"Why? We usually have things under control," Supergirl said, her curiosity piquing.

"The TARDIS usually takes us where we need to be," Martha said, "Or where he needs to be, I just tag along."

"So you're trying to help?" Winn asked.

"Yes, is that too hard to understand?" The Doctor said sounding a bit angry.

"It's just that people don't help or try to get in our way," Winn said.

"Well Supergirl helps out, why can't we?" Martha asked

"Do you have any idea whose ships they are?" Supergirl asked crossing her arms. J'onn joined Alex in the surveillance room, curious as to what was transpiring.

"I have a few ideas but a lot of ships are constructed in similar ways to the ones hanging out above."

Winn and Supergirl exchanged a look.

"Well I'm kind of stumped on what they could be," Winn said, "We could use your help."

"I'd love to help! Allons-y!" They all headed towards the door but the door wouldn't open.

"Hey Alex," Supergirl shouted into one of the cameras, "Could you let us out?"

**Surveillance room**

Alex looked up from her screen and turned towards J'onn, "Why don't you trust the Doctor? He hasn't done anything wrong."

"There's something off about him, Alex. And I don't know what."

"Is it because you can't read his mind?"

"It's something else. Why would a time traveller go around helping people? He could be trying to change the past to benefit himself in the future."

"Then why is Martha from 2007?"

"Maybe it's part of his sick plan."

"I don't think so."

"Alex?" Kara called again from the screen, "You still there?"

Alex sighed, "Can you trust me on this one? Please?"

J'onn sighed and opened the door and left the room with Alex on his heels.

**Control room**

"Wow..." Martha muttered as they walked into the control room, marvelling at the technology and operation they were running here.

"So Winn," The Doctor said, "What do you have so far?"

"Let's take a look," Winn said sliding into his chair and opening up some programs on his computer, "This is one of the scans we have of the unknown ships."

The Doctor crouched behind Winn and put on his glasses, "That's a pretty common type of craft nowadays," The Doctor muttered analyzing the scan, "Is there any way you can get a picture of the ship?"

"Just a second. Bingo!" Winn shouted as he pulled up a blurry photo, "We'll just run in through this software and it should clean it up!"

"Nice going Winn," Supergirl said.

"Thanks, Ka-Supergirl," Winn said catching himself but his little slip up confirmed what the Doctor already thought; Kara Danvers and Supergirl were the same person.

"Supergirl," J'onn said, "Can I have a word?"

"Sure," she said following him into a side room, "What's up?"

"I want you to keep an eye on the Doctor, there's something off about him."

"He seems pretty harmless."

"How many times has someone who 'seemed harmless' hurt us? And I can't read his mind."

"I'll make sure to keep an eye on him, J'onn, don't worry."

"Thank you."

**Control Room**

"You're from 2007 right?" Alex asked Martha.

"Yeah, that's right. I'm guessing you're from 2017."

"Yeah. How did you meet the Doctor?"

"That's a funny story actually. I was training to be a medical doctor when he showed up in my hospital just before it got transported to the moon."

"You were teleported to the moon."

"Not just me, the entire hospital. It turned out the rhino space police-"

"The Judoon," The Doctor cut in.

"-Were looking for an alien fugitive and he helped return us back to Earth just before we ran out of oxygen."

"That's one hell of a story, I'm guessing you've been travelling with him ever since."

"Yeah, I've gotten to see some of the most spectacular things. What about you, how did you meet Kara?"

Alex looked shocked but she tried to suppress it.

"I'm not going to tell anyone. Besides, it's not that hard to figure out. First Supergirl saves us, then Kara comes to interview us a little too quickly. Then Supergirl comes here and says Kara shared everything with her. They looked very alike, then Winn confirmed my suspicion. How did you meet?"

"My parents adopted Kara when her pod crash-landed on Earth when I was 11."

"So you're sisters then?"

"Yup."

"That's amazing!"

"Ah-ha!" The Doctor shouted grabbing Alex's and Martha's attention.

**Notes for the Chapter:**

> Just a heads up next week's chapter might be a bit late because school is going insane. I hope you're enjoying the fic so far.


	6. Chapter 6

**Control Room**

"What is it, Doctor?" Martha asked walking up behind him.

"Do you see the insignia on the side of the ship? It means it's from the Dobranje* galaxy."

"And I have pulled up a list of every known species originating in that galaxy. Well, that we know of." Winn said, spinning around in his chair.

"Hey, I've heard of the Dobranje galaxy," Supergirl said, "But why are they here? Their people usually don't leave their own galaxy."

"That's the question, Supergirl," The Doctor said. He had millions of scenarios playing out in his mind of what they could be doing here, how they got here, what planet they're from. Not a lot of the scenarios were positive, very few of them were.

"Could they be the Zmije*?" J'onn said, "I know their planet has fallen on hard times lately."

"It could be," The Doctor and Winn said at the same time. Winn pulled up the file on the Zmije and their home planet and displayed it on the big screen.

"Wow," Martha mumbled, "They have a lot of alien tech to their name."

"Yeah, a lot of them being weapons," Alex added.

"I guess it's safe to say they're not here in peace," Supergirl added.

"Their planet has recently suffered a catastrophic war with their sister planet, I believe both planets were destroyed," J'onn said.

"And since Earth has a similar atmosphere I'm guessing they're here to take it over," Winn said.

"That would be my guess," The Doctor said absentmindedly. He had pulled out his glasses and was scanning the screen. The DEO had a lot of alien information but there were some gaps in their files, "If you look at their ship it's severely damaged, meaning they're not going to fully assault the planet. There's damage to the hull by the weapons systems and the core. Most of their weapons are either destroyed or they're using the core to power live support instead of the functioning weapons."

"So they're going to try and infiltrate us slowly and attack once they have sufficient ground soldiers," Alex said, "We have to intervene sooner rather than later."

"Alex is right," Supergirl said, "J'onn do you have any ideas?"

J'onn barely heard Supergirl, he was focused on the Doctor. He had just told them more about the Zmije ships than any of them would have known from just reading the file, they didn't even have an image of an undamaged Zmije ship.

"J'onn," Supergirl called again snapping J'onn from his thoughts.

"Since their systems are severely damaged we might be able to send a threatening message and get them to leave peacefully."

The Doctor didn't like the word _Threatening_ but sending a message was much better than launching an attack.

"Winn, can you open up a link with the Zmije ship?"

"On it."

Martha walked over to the Doctor and whispered, "They're not going to let us go are they?"

"No, they would have let us go already, they wouldn't want us seeing their operation. I'm sorry Martha, they're keeping us here because of me."

"Don't worry, Doctor, it's not your fault. This operation is really interesting."

"Interesting and deadly."

"Ready when you are J'onn."

J'onn turned to face the screen and Alex and Supergirl stood on either side of him. Winn, the Doctor, and Martha were obscured in the background but parts of them could still be seen.

"This is J'onn J'onzz calling you from Earth. Identify the nature of your visit. We are armed and ready to fire at any hostile actions."

Winn typed a few commands and ended the transmission, "I think that struck the balance of welcoming and threatening very well."

"Now we've just got to wait for a response, yeah?" Martha asked. Alex nodded.

"Hey, Winn. How did you find the ship's frequency so quickly?" The Doctor asked, "Using 21st-century technology it should have taken you at least an hour."

"Well, I used some alien tech from various species."

"Wow, can I take a look?" Winn nodded then started spewing high-grade technobabble to which the Doctor responded with even more technobabble.

"Those two are really getting along," Supergirl whispered to J'onn.

"I know. I don't like it, this Doctor seems to know everything about these aliens. I'm starting to think he is one."

"Any species in mind?"

"No. But I do believe that he's a time traveller, only because Martha confirmed it."

"So he could be any species past, present, or future. That narrows it down."

"What's life like in 2007?" Alex asked walking up to Martha.

"I don't know, normal I guess. After seeing the things I've seen with him my life in 2007 seems so... mundane."

"What have you seen?"

"After the who Judoon incident, he took me to see Shakespeare to thank me for resuscitating him."

"He took you to a play? Seems like he's trying to, you know..."

"I wish, but he's still hung up over Rose. And he didn't take me to a play, we went back and met Shakespeare and watched his lost play."

"What was it like?"

"Well the play was written by aliens trying to get the rest of their kind out of prison, but the Doctor and I stopped it."

"Hey, J'onn! We've got a response!"

"What did they say?"

"I don't know, their language isn't in the database, it's going to take a while for me to translate."

"You don't need to translate it," The Doctor said looking a little frightened, "It says 'prepare for transport.'"

Just as the Doctor said that a blue light surrounded all of them.

"Doctor what's going on!?" Martha shouted.

"They're teleporting us onto their spaceship."

Then Martha saw a blinding flash of light and closed her eyes tight. She had a throbbing headache and had ended up on the floor. When she opened them she was no longer in the DEO.

"Doctor?" She called. No response. "Doctor?" She called again.

"Martha? Is that you?" Someone called, it certainly wasn't the Doctor, "It's Winn. Are you alright?"

"Yeah I'm fine," Martha blinked a few times, "Are you okay?"

"Yeah. Do you think we're on their spaceship?"

"Yeah," Alex said from across the room, "My question is where's Kara? And why did they separate us?"

"The Doctor and J'onn are missing as well," Winn pointed out.

"So that's our priority, finding Kara, J'onn and the Doctor," Alex said, "Let's find a way out of this room then navigate the ship from there."

For the first time, they took a proper look at their surroundings. This part of the ship was very high tech with alien-looking computers in the walls and with what could only be described as futuristic tools covering tables and filling up cabinets. Winn was obviously attracted to the computers in the wall and immediately started learning the alien computer language.

Alex started coming up with an exit strategy, for one to work she needed to find a door or a hatch or a vent big enough for them to crawl through. It wasn't a big room, she should have found something by now.

Martha started looking at some of the tools lining the table, she didn't know much about alien tech but she could've sworn that the alien tools looked like medical equipment.

"Woah," Winn muttered, "You might want to take a look at this," He said to no one in particular. Martha and Alex both made their way over and took a look at the screen.

"Those are our heart rhythms," Martha said pointing at the 3 lines on the screen, "And I'm assuming that the other readings are monitoring us as well."

"I agree," Alex said.

"Why are they monitoring us?" Winn said a bit panicked, "What could they gain by monitoring us?"

"I can't answer that," Martha said, "But I think I know why they separated us. They separated the humans from the aliens."

"So they're probably monitoring us to figure out a biological weakness they can exploit," Alex added.

"So we're basically guinea pigs," Winn said.

* Dobranje is pronounced DOE-brawn-yeah; Zmije is pronounced ZMEE-yeah


	7. Chapter 7

**Notes for the Chapter:**

> Happy Family Day everyone! It may not be Family Day in other countries but it is in Canada, so even if you're not Canadian hang out with your family even more today! It is also international fanworks day! Have a wonderful day and enjoy!

**Zmije Ship**

Kara stood up holding her head, she was experiencing the worst headache of her life. She blinked her eyes a few times to clear her vision and saw J'onn getting up off the ground but the Doctor looked unaffected. He was closely analyzing the walls of what looked like a cell with a thing that was making a buzzing noise. It was making her headache worse.

"Doctor, could you stop that?" She asked.

"Oh, sorry," He said stopping the buzzing noise, "Forgot Zmije teleports can have nasty side effects. How are you doing?"

"I'm fine. I've just got a really bad headache."

"Don't worry, it will pass. How are you doing J'onn?"

"I'm telepathic and mostly unaffected by rough teleports."

The Doctor paused for a moment, then smacked his forehead, "Of course! You're a Green Martian! With a name like J'onn J'onzz and telepathic capabilities, how could I miss that!"

J'onn and Supergirl looked at each other.

"Sorry, I can be a bit thick sometimes. My question is where are the others?"

"I have a few more questions than that." Supergirl said, "Like why did they separate us? Why did they choose the groups that they did?"

"I can answer that one Supergirl," J'onn said, "I think they separated the humans from the aliens."

The Doctor looked a little surprised while J'onn and Supergirl looked offended. The Doctor's brain was trying to figure out a way out of this one, Kryptonians did not like Time Lords.

"Well... You're right about that," The Doctor said scratching his chin. Then the room filled with an awkward silence.

"Are you going to tell us your species?" Supergirl asked.

"I'd rather not," The Doctor said turning back to the wall and pulling out his sonic screwdriver. Supergirl was now very pissed off, between losing Alex and now this 'Doctor' hiding something major from them, she lost her temper. She stormed across the room and shoved the Doctor up against the wall.

"Oi!" He shouted.

"I will not ask you again, what species are you?"

"Well, you just contradicted yourself and asked me again," Supergirl just shoved him up against the wall harder, "Alright alright. You can stop, I don't like violence. Let me go and I'll tell you."

Supergirl held him against the wall, she did not want to let him go.

"Supergirl," J'onn warned. As much as J'onn didn't trust the Doctor he had a feeling he was telling the truth. Supergirl didn't want to let him go, she had a feeling that he would cause them problems, but she relented and let him go.

"Thank you," The Doctor said stringing his jacket, "You've got to know, I'm not like my people," The Doctor paused. During the pause, J'onn's and Kara's brains were thinking about what species needed an introduction like that. They certainly weren't expecting the answer they received.

"I'm a Time Lord."

**Lab**

Winn's heart was racing, "How are they monitoring us? it doesn't make any sense. W-we have no leads on us. Did they put an implant in us?"

Martha and Alex exchanged a look, they had the same questions that Winn had but they weren't freaking out. It was evident by their heartbeats on the screen.

"Winn, calm down," Alex said, "Panicking isn't going to help. We have to focus on finding Kara."

Martha could tell that Alex was really worried, of course, Martha was worried about the Doctor but she knew he would find a way out, he always did.

"Our first step to finding Kara, J'onn and the Doctor is finding a way out of this room. Winn, you take a look at the tech and see if you can find anything useful. Martha, can you scan the walls and see if I missed a door or another exit point."

"On it," Martha said slowly walking around the room.

Winn made his way over to a table and started looking at all of the tech, he was unfamiliar with Zmije technology but he had to find a weapon or something to get us out of the room.

Alex made her way over to the computer, she had noticed something weird on the ceiling; it was like a half-dome with 3 short prongs sticking out of it. She had two theories to what it could be, it was either what was monitoring them or what teleported them in here.

**Prison Cell**

Supergirl shoved the Doctor up against the wall again, "You could have saved Krypton!"

"Supergirl, let him go," J'onn said.

"We helped you in the war! And you let us perish!"

"Kara!" J'onn shouted.

Supergirl reluctantly let the Doctor go, but she wanted to punch him so hard.

"I'm so sorry about Krypton. I really am-"

"Your people were never sorry about anything, don't lie to me." Supergirl was staring daggers at the Doctor, her hands clenched in fists beside her, "As soon as you mentioned your TARDIS I should have known you were a self-entitled Time Lord."

J'onn had just been watching the interaction; he had heard whispers Time Lords and the Last Great Time War but he didn't know as much as Kara did. He looked at the Doctor and saw an expression of sadness cover his face and a hint of pain in his eyes. There was a lot more to this man than meet the eye.

"Listen, I just want to save Martha and your friends, then I'll be gone. You can forget I ever came here."

"I doubt you're capable of saving anybody," Supergirl snorted.

J'onn saw the layer of pain grow in the Doctor's eyes, despite his attempt to hide it. Now there was a hint of anger in there as well.

The Doctor was doing his best to keep from lashing out, but it wasn't easy. His people had betrayed the Kryptonians and he wasn't able to save it. And some days it felt like he wasn't capable of saving anybody.

"Martha is a good friend of mine, I'm not going to let anything happen to her. If you don't want to help me that's fine, but don't get in my way," The Doctor said in a very cold tone.

Supergirl was about to take another jab at the Doctor when J'onn stepped in, "How can we trust you, Doctor. From everything Supergirl has said and rumours I've heard, I'm not inclined to trust you either."

The Doctor sighed, "Read my mind, J'onn. I'm not lying."

J'onn began to read the Doctor's mind, he could see how concerned he was for Martha and the plans he was forming. His mind moved really fast. J'onn also felt the effects Kara's words had on the Doctor, waves of pain, sorrow, and guilt. But the Doctor wasn't lying, he wanted to save Martha, Winn, and Alex and he wanted to send the Zmije away from Earth. J'onn wanted to figure out why and pushed further, but he hit a wall. _I don't want you in my memories, J'onn._ The Doctor said to him, and he understood, he wouldn't want the Doctor in his memories either.

When J'onn started to read the Doctor's mind, the Doctor tried to read J'onn's thoughts. He couldn't help it, but all he got was a sense of J'onn's curiosity. Perhaps if he pushed harder he could get some sort of information from him but he decided not to in case J'onn caught him.

"I trust him, Kara. He's not lying."

Kara looked a bit baffled, she knew the Time Lords as a back-stabbing race.

The Doctor took out his sonic screwdriver and started scanning one of the walls, "Do you guys know anything about Zmije's ships?"

"No."

"Well, the ships usually travel in fleets with the main ship and smaller side ships used for recon or storing things not needed often."

"Like prisoners?" Supergirl asked.

"Exactly. Because of this format, they needed a way to travel between the ships-"

"So they made a teleport system," J'onn said.

"Yup," the Doctor said moving to another wall.

"But why not keep the smaller ships in the bigger one then?" Kara asked.

"The Zmije had a hard time creating a shielding system. So they used the smaller ships as shields."

"If the ships were filled with prisoners then the attackers could kill the people they're trying to save," Supergirl said.

"Exactly! You're a smart one, Supergirl. To prevent other species from using their teleport system they used one that tunes to DNA. If they don't like the species that enter the teleport then it will change their destination. Which is why we ended up in here and our human friends are elsewhere."

"You certainly know a lot about the Zmije, Doctor."

"Not really, I just know a lot about their technology. Ah-ha!" The Doctor stopped the beeping of the sonic screwdriver and a door opened.

"How did you open that?" J'onn asked.

"With my sonic screwdriver."

"Who looks at a screwdriver and thinks 'this could be more sonic'?" Supergirl asked.

"I did."

Supergirl just looked at the Doctor, she still didn't trust him completely, but he had just gotten them out of their cell. A show of good intentions was all it was, he was still a back-stabbing Time Lord.


	8. Chapter 8

**Notes for the Chapter:**

> And I'm back again with a new chapter! I'm pretty happy with this one too. We just had a large snowfall where I live so drive carefully and stay safe. But it's nice having bigger snowfalls in February than in April for a change. Any and all feedback is welcome, so enjoy!

**Lab**

Martha had searched the entire room three times and found nothing, not even a tiny air vent. Maybe it wasn't meant to have air vents, maybe it was designed as more of a closet. The walls were pretty bare, but that could also be because it was an alien spaceship. She just wanted to find the Doctor and get out of here.

"Find anything, Martha?" Alex asked, turning away from the computer in the wall.

"Nothing, and I've checked three times."

"What about you Winn?"

"I don't know much about Zmije tech but this looks like a blaster," Winn said holding up something that looked like a piece of scrap metal, "And it should bust right through the wall."

"Are you sure?" Alex asked as Winn pointed the scrap metal thing at the wall.

"Not really, but it's worth a shot. No pun intended."

"If we're not sure it's going to work then let's not use it. I don't want to end up vaporized to something," Martha said.

"It's our only shot of getting out of here alive, and I don't do well in small places," Winn said.

"I think we should try it. I understand the risks, but the longer we stay in here the more information we give the Zmije. Go for it, Winn."

"All right, stand back. I don't know how powerful this is gonna be." Winn took a deep breath and pulled the trigger. It sent a green laser beam speeding towards the wall, but instead of breaking down the wall, the beam bounced back at them. Luckily for Winn, he was standing at a slight angle and the beam missed him, but it grazed Alex's arm. The beam then hit a weird nook in the wall and bounced a few more times and then stopped.

"Alex! Are you alright?" Winn asked running over to her.

"I'm fine, I think it just grazed me."

"I'm so sorry."

"Here let me have a look," Martha said grabbing Alex's arm, "It looks like a second-degree burn. You're lucky it's not worse. Winn, can you see if you can find me any water and bandages?"

Winn started looking through one of the cupboards on the walls looking for the supplies Martha needed.

"Martha I'm fine, I've had worse."

"I want to keep this burn from getting worse." Winn handed Martha something that looked to be water, "Now hold still." Martha poured the water over her wound then wrapped it up neatly. Alex looked over Martha's handy work.

"You'll make a good doctor, Martha."

"That's only if I can pass my exams."

"You'll do fine."

There was a quiet beep from the computer in the wall and Winn ran to check it out.

"Hey Alex, there's a new symbol by your stats."

"Really?"

"It must be because of your injury. I'm sorry about that."

"Don't worry about it, Winn. None of us knew it was going to happen."

"We should probably stop fooling around with their tech though. The Zmije probably just want us to hurt ourselves to learn more about us."

"Good point. I will no longer touch their tech. I cross my heart."

"Let's just hope Kara and J'onn can get us out of here."

"Me too," Winn said sliding down the wall onto the floor.

"Where are you, Doctor?" Martha muttered.

**Prison ship**

_"Unauthorized cell breach!"_ The speaker said from all around them.

"Well, that's not good," The Doctor said.

"Can't you just shut it off with your sonic screwdriver?"

"I could if I could figure out where the speaker is."

"You're not going to have time for that Doctor," J'onn said, "We've got company." There were four Zmije guards running down the hallway with rather large laser blasters.

"Run!" The Doctor said taking off down the hallway.

"Why are we running? We can take out those guards," Supergirl shouted at the Doctor as they rounded a corner.

"You and J'onn might be able to take them but I can't."

Supergirl snorted, "A Time Lord being peaceful, what else is new?"

But the Doctor didn't seem to notice the comment, "And we're looking for one of these. A teleport matrix!"

"Why didn't we just use the one in our cell?" J'onn asked.

"Because these types of teleports can have nasty settings, I didn't want to accidentally trip one of those and sending us somewhere far away from Earth."

"You fiddling with this box isn't going to stop the guards."

"I just need a minute."

A laser blast flew down the hallway as Supergirl peaked around the corner, "You don't have a minute," she said.

"But we can give you a minute," J'onn said transforming into his true Green Martian form.

He nodded at Supergirl and they burst around the corner. They each disarmed a guard with ease and it became a punching match with the other two guards not wanting to hit their own.

The Doctor was working away at the teleport matrix overriding programs and disabling safeguards with his sonic screwdriver. He could do a better job with more time as he couldn't use the same coordinates as before without risking Martha and friends' lives.

"I've got it! Hold on!" The Doctor shouted and with one more bleep of his sonic screwdriver the teleport activated and they were sent back to Earth.

**Alleyway**

Supergirl almost lost her balance but the teleport wasn't too bad the second time around. She looked up and saw the J'onn had changed back into his human form. She also noticed that they weren't in the DEO.

"Why aren't we in the DEO?"

"I couldn't risk using the same coordinates in case there was a fail-safe to direct us somewhere else. And before you ask about your friends I couldn't grab them without using the same coordinates."

"Why didn't you just teleport us onto the main ship?"

"We get onto the main ship then what? If we find our friends then teleport back then how do we get rid of the Zmije? I don't think a human could survive two trips back to back in a Zmije teleport."

"What's your plan then, oh great Time Lord?"

"Whatever your plan is, Doctor, let's discuss it somewhere else. I don't want the Zmije finding our location." J'onn cut in before someone said something that they would regret.

"Let's head back to the DEO and sort figure out our next steps there."

"I think you've forgotten that the DEO is also compromised," the Doctor cut in, "Why do you think I teleported us here in the alley?"

"Because you got the coordinates of the DEO mess up."

"No, and I didn't even use coordinates to get us here. I was looking for traces of Artron energy and since I forgot to close the engines of my TARDIS there was a large enough signature to lock onto."

"Can't the Zmije do the same thing?" J'onn asked.

"Well, yeah. But Artron energy isn't a common energy trace to look for and if I close my engines there won't be a large enough signature to lock onto."

"Hold on a minute, is this just one big ploy to get us onto your ship? There's no way I'm stepping into your TARDIS or whatever."

"I never said you had to come," the Doctor said and turned towards his TARDIS.

J'onn had had enough of Supergirl trying to get a rise from the Doctor. He could almost feel the effects of Supergirl's words radiating from the Doctor.

"Kara, what's gotten into you?"

"Well sorry if I'm being rude but his people cause so many problems in the universe it's about time someone disrespects them."

"He's just trying to rescue his friend and he also happens to have a way to get back onto the ship."

"Whatever happened to figuring this stuff out ourselves? We don't need his help."

"He's offering to help and knows significantly more about the Zmije than any of us. Can you put aside the fact that he's a Time Lord and focus on saving Alex and Winn?"

Supergirl sighed, "Fine, but I still don't trust him. And when this is over we're all going to have a nice long chat."

J'onn walked over to the blue police box the Doctor had walked into earlier; it was an odd-looking spaceship, to say the least. There was no way all three of them were going to fit without a yelling match starting up. J'onn hoped for the best and knocked on the door.

**TARDIS**

The Doctor had just finished closing the engines when he heard someone knock on the door. He was hoping that Supergirl would have left and he could save Martha on his own. Her sly comments about Time Lords were bringing back some memories he wished he could forget. But he would probably need their help on the ship; the Zmije were known to be violent, he was not. He reluctantly walked over to the door and opened it just enough so he could be seen fully but the interior of the TARDIS stayed hidden.

"Do you have a way to get back on the ship and save our friends?" J'onn asked. At least it was J'onn asking and not Supergirl.

"Yeah, and I have a plan. Well, part of a plan. But it's all the same. And I could probably use your help."

"As we could use yours. Is this your Spaceship?"

"Yeah, come on in."

"Maybe it's best we discuss our plan out here, we would be pretty cramped in there."

"Na. Come on in!" The Doctor said and a wide grim beamed off of his face as he stepped away from the door letting J'onn and Supergirl into the TARDIS.


	9. Chapter 9

**Notes for the Chapter:**

> Hey everyone, sorry I'm updating a bit late I was making a chicken casserole then cleaning the kitchen after making said casserole. What can I say, I'm a messy cook. I hope you enjoy the chapter, any feedback is welcome!

**TARDIS**

The Doctor leaned up against one of the poles waiting for J'onn to enter his TARDIS; no matter how bad a day he was having he always loved this part.

J'onn looked over at Supergirl before squeezing into the TARDIS. But he didn't have to squeeze. He took a few more steps into the box then stopped. He felt a weird psychic presence coming from the TARDIS but he wasn't sure. But he still looked around the TARDIS in awe.

"I was not expecting this..."

Upon hearing this Supergirl stepped into the TARDIS and stopped dead in her tracks.

"What the... This should be impossible." She knew that TARDISes were beyond her people's understanding but she didn't know that they were bigger on the inside.

The Doctor had a big smile on his face. None of them had said the iconic line but their shocked expressions were enough to make the Doctor's day.

"Now," The Doctor said sprinting to the console, "Let's go find our friends."

This was apparently enough to break J'onn and Supergirl out of their respective trances.

"So you're gonna fly us up to their ship?" Supergirl questioned, "Assuming we get through their defences in this wooden box how will we even find our friends? Their ship is huge."

"When I teleported us off of the Zmije ship I grabbed the teleport link coordinates, they should lead us right to them," The Doctor said while running around the TARDIS console pushing buttons seemingly at random.

"But that doesn't solve the Zmije defence problem, Doctor," J'onn said, "They'll see us flying in and turn your ship into pieces."

"Who said anything about flying?" The Doctor said with a grin and pulled down the big leaver.

The TARDIS lurched, causing everyone to stumble. Then she began to wheeze.

"What's going on?" Supergirl shouted.

"We're dematerializing!" The Doctor replied with a huge grin.

J'onn and Supergirl exchanged a confused look, Karas was more annoyed than confused but she promised J'onn that she wouldn't speak to the Doctor unless completely necessary.

The TARDIS shuttered a few times but there were no huge lurches, she must have been happy that the Doctor closed her engines to let him have such a smooth flight.

The wheezing noise stopped then a cloister bell rang. The Doctor ran around the console pulling the screen with him checking the coordinates.

"We seem to have landed in the right place," The Doctor muttered rubbing his chin. He walked over to the pole where he usually threw his jacket and put his jacket on. Just as he was about to head for the doors J'onn stopped him.

"Do you have any sort of plan Doctor?"

"Well, find Martha and friends to start."

"How do you plan to find them?"

"Wander around I suppose, it's always worked for me."

Supergirl did her best to hold in a scoff, where did a Time Lord wander around anyway? It's not like they ever left Galifrey except to fight in that stupid war.

"Supergirl, can you use your advanced hearing to try and listen for them?" J'onn asked.

"Good idea, J'onn."

 _How come I didn't think of that?_ She asked herself, her sister was the one in danger anyway.

"Now that we've got that sorted out, allons-y!" The Doctor smiled, and then sauntered out of the TARDIS with his hands deep in his pockets.

J'onn and Supergirl followed him out, however, they were a bit skeptical, the Doctor's spaceship was more impossible than J'onn's, and that was saying something. Needless to say, they were a bit surprised that the TARDIS was now on the Zmije ship.

Supergirl took a deep breath and began to listen, the almost unnoticeable creaks and groans of the Zmije ship were amplified, it was like the ship was crying. It wouldn't survive much longer in its current state of disrepair. She listened closer until she heard the unmistakable British voice of Martha.

_"So what's it like to work for a top-secret government agency?"_

_"Amazing!"_ Supergirl heard Winn reply.

"This way," Supergirl said to J'onn and the Doctor as she took off down one of the hallways.

**Lab**

"Amazing! You get to save people from things they don't even know exist. And you get to play around with alien tech when you're not busy dealing with alien threats," Winn said. Martha's eyes sparkled, the thought of saving people from alien threats is exactly what she did with the Doctor and it is was she loved. The only thing she loved more was the idea of becoming a medical doctor.

"But you have to be careful too," Alex said, "Top-secret jobs are hard, you can't tell people you work for them. For the longest time, I had to lie to Kara about where I worked. It was hard and this was before she became Supergirl."

Martha thought for a moment, she found it hard enough lying to her mother that she was travelling with the Doctor, she couldn't imagine lying to her about her job..

Her thoughts were interrupted by a wall smashing in. Alex, Winn, and Martha all stood up as quickly as they could expecting some angry Zmije, but instead, they saw the blue and red figure of Supergirl.

"Kara!" Alex shouted.

"Alex," Kara said running over to give her a hug, "Are you alright?"

"I'm fine."

"Ah Ms. Jones," The Doctor said walking up to Martha, "Did you have a good stay in a Zmije laboratory?"

"No," Martha scoffed. Then she smiled, "I'm glad to see you though," she said giving him a hug.

J'onn just stood in the 'doorway' and nodded his head, "Agent Schott."

"Hey, J'onn. So, what's the plan?"

The room went silent as everyone came up with their own plans but the Doctor was the first to speak.

"Let's go find the Zmije leader and give them a talking to."

"You're going to need a plan B," Supergirl retorted.

Martha and Alex looked between Supergirl and the Doctor, it was pretty clear that Supergirl hated the Doctor, no matter how much she tried to hide it.

Winn noticed the tension as well but was more concerned with pulling up the schematic of the ship.

"Hey, I've got the schematic of the shipped pulled up."

The Doctor came over and put on a pair of brown glasses and studied the screen. By the time Martha had taken a good look at it, the Doctor had it memorized.

"If we go through the hallway the TARDIS is in and turn left we'll be in the control room."

Winn was surprised by how quickly the Doctor came up with but he quickly confirmed the Doctor's theory.

"What use is being in the control room if we don't have a plan?" Supergirl asked.

"I do have a plan."

"Talking the Zmije out if taking over the Earth is not a plan."

"Of course it's a plan, it's always my plan."

Supergirl snorted, "It's not much of a plan."

Martha realized that this bickering could go on for a while and stepped in, "If we're in the control room we can take over the controls if talking them out if it doesn't work."

The Doctor was silently thankful for Martha, Supergirl was getting on his last nerve.

Alex was thankful too, it was quite embarrassing for Kara to be acting this way, the Doctor seemed nice even though they weren't sure if they could trust him. Alex looked over at J'onn and he looked annoyed, probably by Kara's bickering.

"I have an idea," Winn said, "How about we just head over to the control room and come up with a plan B on the way?"

Everyone turned to look at him but he didn't care, there was so much tension in the room he wanted to get out. He was pretty sure everyone else wanted out too but Kara looked pretty upset.

"You're taking his side?" Supergirl asked

"I'm not taking anyone's side, just making a suggestion."

"I agree with agent Schott," J'onn said looking around the room, "What do you think agent Danvers?"

"I agree with Winn as well."

"Right then, let's go to the control room."

The Doctor was tempted to say, allons-y but decided against it, Supergirl was already staring daggers at him and he didn't want to make it worse.

J'onn led the way out of the room followed by the Doctor and Martha. Winn followed quickly hoping to ask the Doctor about some Zmije tech. Alex stopped Supergirl from leaving.

"What's gotten into you?" She asked, "Did I miss something between you and the Doctor?"

"He's a Time Lord swine. His people could have saved Krypton but they were too busy with their petty war to care about us when we became useless to them."

"Kara can you put that aside for now, we have more pressing problems."

"How can you trust him? My people did and where did they end up?"

Alex was taken aback by Kara's anger, but then a thought came to mind, "If his people are involved in a war then why isn't he taking part in it? Maybe he's not like the other."

Kara scoffed, "Yeah right. All Time Lords-"

"We've got to move before we lose the others," Alex said picking up the Zmije blaster.

Supergirl was still angry with the Doctor but Alex did make sense, the Doctor was not as stuck up as Time Lords usually were. But it still doesn't change the fact that he and his people could have saved Krypton.


	10. Chapter 10

**Notes for the Chapter:**

> Here is the next installment of my fic! It's mostly filler but I promise the next chapter will be exciting! Thank you for reading this, you officially made it 10 chapters in! Please enjoy!

**Zmije Ship**

"Doctor are you alright?" Martha asked doing her best to keep up with the Doctor.

"Of course I'm alright, why wouldn't I be?" The Doctor said keeping a straight face but there was darkness in his eyes.

"It looks like something happened between you and Supergirl. So am I going to have to ask her what happened or..."

The Doctor sighed, he knew Martha wouldn't stop asking until he gave her answers, "She thinks that my people, the Time Lords, could have saved her planet. We could've, I could've but with the war in its final days... there was nothing we- nothing I could do," the Doctor paused to suppress memories of the war that were trying to surface, "A lot of planets were lost because of the war, Krypton was just one of them."

Martha was silent, it was rare to hear the Doctor talk about the war or his past in general. She could see how sad he was but he did his best to hide it, Martha could only imagine what the war must have been like.

"She's one of the lucky ones too," The Doctor said nodding, "Not only did she survive with her cousin, but other species still know that Krypton existed. That's luckier than some other species..."

The Doctor went silent again. He took a deep breath and cleared all of the bad memories that were popping up. He wiped away the emotions of pain and guilt and sorrow off of his face. He could deal with those later.

He had been telling himself that ever since he ended the war all those years ago.

Neither of them noticed Winn eavesdropping on their entire conversation.

They rounded the corner and saw J'onn waiting by the TARDIS for the rest of the group to catch up.

"It's really a spaceship then," Winn said gesturing to the TARDIS.

"Yes she is, she's a marvellous one too."

"But how does it even fly? It's too small to contain a propulsion system and two passengers?"

"Well," the Doctor began but was cut off.

"I have a plan B," Supergirl announced coming around the corner, "What if we force the ship to leave Earth's orbit and lock the controls?'

"I like that idea," Winn said, "But I don't know my way around Zmije tech too well."

"You figured out how to use their computer back in the lab, I'm sure you could figure out the controls," Martha said.

Winn smiled.

"You know what I find odd," the Doctor said, "We haven't seen any Zmije guards or heard any alarms. You'd think they'd be keeping a closer eye on us."

Everyone went silent.

"This is probably what they want," Alex said, "For us to go and challenge them."

"But we don't have any other choice," Supergirl said, "We take the fight to them."

"Agreed," J'onn said, "But let's stick with our plan A, we don't know what kind of firepower they have or how many Zmije will be in the control room."

"Alright, let's do this," Supergirl said.

The Doctor contemplated asking Martha to stay behind in the TARDIS but the determined look on her face stopped him. Besides she would take his side if things went pear-shaped.

Winn was processing what the Doctor had said about the war, how could you be lucky that your planet was destroyed? What did he mean by _other species still know that Krypton existed_? What did he have to do with it? There was a lot more to the Doctor than met the eye, that was for sure.

He wanted to tell Kara but this definitely wasn't the time, she was already angry enough that the Time Lords didn't save Krypton, she didn't have to know that the Doctor could have. There was also no way he could keep this to himself. Sometimes he hated his big mouth.

Martha was nervous and excited at the same time, it was always like this travelling with the Doctor and it's why she loved it. She still couldn't believe there was a whole agency dedicated to the extraterrestrial. But it made sense, Earth isn't the only planet the Doctor protects, he can't be here all the time even though he has a time machine. The DEO was a lot more professional and orderly than the Doctor with a clear mission and objective. The Doctor just shows up, acts like he owns the place, and solves whatever problems happen to arise. _What would it be like to work for the DEO?_ She thought.

The Doctor would usually be full of energy like a child confronting an alien race but not this time, he was too tired. All of Kara's comments and the memories that they brought out were wearing him down. He wanted to shout at her, he wanted to get angry with her but he couldn't. Doing that would mean reliving the Time War and he didn't want to deal with those memories. Besides, now wasn't the time, he had another planet to save.

Kara was just trying to push down her feelings of resentment and hatred away. She hated the Time Lords and everything they stood for, but Earth needed her right now; she couldn't give up on it. She would do everything she could to save her new home. To save Winn's home. To save Alex's home. She would not let it be destroyed like Krypton, she didn't want Alex and Winn to live through losing their home planet. She didn't want anyone else to go through that pain.

Alex was worried about Kara, she could be a hothead sometimes and now was no time for her to lose her temper. She felt bad for snapping at Kara back in the lab but there were-and are-more pressing concerns. She just hoped that Kara would not lose her temper when it mattered most.

They all gathered outside the control room door, everyone pushing aside their thoughts to get ready for whatever lies ahead. Alex pulled out her Zmije blaster and the Doctor pulled out his sonic screwdriver. Winn and Martha stood behind everyone else as they had no weapons of their own and were just there as tech support and motivation.

"Ready?" The Doctor asked.

J'onn nodded and Supergirl straightened her back making herself look more imposing than her clothing would suggest.

The Doctor used his sonic to open the door and they walked into the control room.


End file.
